fixed too many partial CDS bug

Former-commit-id: d733a46f4e92f755f38e452f03a28062de6739f1
Former-commit-id: 36bdc324d2b9a0491d07d40a7e68a4cf7ea73984

detectors/cds/tools/compare/go_compare.sh

@@ -34,12 +34,12 @@ endif
 Notify "get genome info from $RefFile"
 
 $AwkCmd -f $LIB_DIR/$RefType.oneliner.awk $RefFile |\
-$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$RefType.cds.awk > R_$$
+$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$RefType.cds_short.awk > R_$$
 
 Notify "get prediction info from $PrdFile"
 
 $AwkCmd -f $LIB_DIR/$PrdType.oneliner.awk $PrdFile |\
-$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$PrdType.cds.awk > P_$$
+$AwkCmd -f $LIB_DIR/libutil.awk -f $LIB_DIR/$PrdType.cds_short.awk > P_$$
 
 #
 # compare

detectors/cds/tools/lib/libutil.awk

@@ -2,6 +2,40 @@
 # utilities library
 #
 
+END {
+  if (_ForceExit_) exit(_ForceExit_)
+}
+
+function Notify(key, msg) {
+    print "# " key " " msg >> "/dev/stderr"
+}
+
+function Info(msg) {
+    Notify("info", msg)
+    return 1
+}
+
+function Warning(msg) {
+    Notify("warning", msg)
+    return 0
+}
+
+function Exit(status) {
+    exit(_ForceExit_ = status)
+}
+
+function Error(msg, status) {
+    Notify("error", msg)
+    Exit(status ? status : 1)
+}
+
+function Assert(condition, msg, status) {
+    if (! condition) {
+      msg = FILENAME ":" FNR ": " msg
+      return status ? Error(msg, status) : Warning(msg)
+    }
+}
+
 function Min(a, b) {
   return (a < b ? a : b)
 }
@@ -10,6 +44,24 @@ function Max(a, b) {
   return (a > b ? a : b)
 }
 
+function Trim(s, regexp) {
+  if (regexp == 0) regexp = "[ \t]+"
+  gsub("^" regexp "|" regexp "$", "", s)
+  return s
+}
+
+function TestPath(path, test, _local_, stat) {
+  if (test == 0) test = "-f"
+  if (Trim(path) == "")
+    return 0 # because of a bug in 'test'
+
+  gsub(" ", "\\ ", path) # protect spaces
+  stat = system("test " test " " path)
+  return stat ? 0 : 1
+}
+
+# ---
+
 function Strip(s) {
   gsub("complement|join|order|\\)|\\(|<|>| ", "", s)
   return s
@@ -106,6 +158,30 @@ function GeneFamily(s) {
   return s
 }
 
+# ---
+
+function ReadFasta(file, _local_, seq, context) {
+  context = $0
+  seq = ""
+  getline < file
+  while(getline < file) seq = seq "" $0
+  $0 = context
+  return seq    
+}
+
+function PrintFasta(seq, name, CharPerLine, _local_, i, len, rest, chunk) {
+  if (CharPerLine <= 0) CharPerLine = 60
+  print ">" name
+  len = length(seq)
+  rest = len % CharPerLine
+  chunk  = (len - rest) / CharPerLine
+  for (i = 0 ; i < chunk ; i++) 
+    print substr(seq, (i*CharPerLine) + 1, CharPerLine)
+  if (rest != 0)
+    print substr(seq, (chunk*CharPerLine) + 1, rest)
+}
+
+
 #
 # constants
 #